Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Gene description Rank Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1025 to 1074 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] 697 FTH1 220.444 209.113 1.05419
    ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] 712 FTHL17 220.431 209.123 1.05407
    ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] 709 FTL 220.438 209.118 1.05413
    ferrochelatase, mitochondrial precursor (ec 4.99.1.1) (protoheme ferro-lyase) (heme synthetase). [swissprot;acc:p22830] 3185 FECH 0.00001 0.00001 1
    fetal brain protein 239 (239fb). [swissprot;acc:q15777] 2339 MPPED2 229.258 230.294 1.00452
    fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] 748 FBL 245.246 233.483 1.05038
    fibrillin 1 precursor. [swissprot;acc:p35555] 2844 FBN1 0.00001 0.00001 1
    fibrillin 2 precursor. [swissprot;acc:p35556] 2955 FBN2
    fibrillin 3. [refseq;acc:nm_032447] 2939 FBN3
    fibulin-1 precursor. [swissprot;acc:p23142] 2349 FBLN1 192.348 191.503 1.00441
    fibulin-2 precursor. [swissprot;acc:p98095] 2245 FBLN2 191.618 190.448 1.00614
    ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] 40 FCN2 322 253 1.27273
    fidgetin-like 1. [refseq;acc:nm_022116] 2078 FIGNL1 215.511 213.814 1.00794
    filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 191 no value 226.582 198.444 1.14179
    filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] 186 FLNB
    fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] 1045 FIP1L1 115.817 119.432 1.03121
    fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [swissprot;acc:p20071] 1375 FKBP1A 216.542 211.908 1.02187
    flap endonuclease-1 (ec 3.-.-.-) (maturation factor 1) (mf1). [swissprot;acc:p39748] 2831 FEN1 0.00001 0.00001 1
    flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] 541 MICAL2 222.156 208.201 1.06703
    flotillin-1. [swissprot;acc:o75955] 1289 FLOT1 218.368 213.22 1.02414
    folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] 1224 FPGS 225.906 231.524 1.02487
    forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 196 FOXP4 263.215 231.407 1.13745
    forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] 619 FOXG1 214.256 202.139 1.05994
    forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 197 FOXP1 263.215 231.407 1.13745
    forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 198 FOXP3 263.191 231.394 1.13741
    formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 178 no value 226.887 194.72 1.1652
    fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 46 FOSL1 204.642 161.068 1.27053
    fos-related antigen 2. [swissprot;acc:p15408] 44 FOSL2 204.641 161.046 1.2707
    fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [swissprot;acc:q06787] 1828 FMR1 202.41 200.115 1.01147
    fragile x mental retardation syndrome related protein 1. [swissprot;acc:p51114] 1825 FXR1 202.386 200.086 1.0115
    fragile x mental retardation syndrome related protein 2. [swissprot;acc:p51116] 1823 FXR2
    frg1 protein (fshd region gene 1 protein). [swissprot;acc:q14331] 2745 FRG1 201.476 201.514 1.00019
    fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] 2561 FBP1 209.825 210.18 1.00169
    fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 2551 FBP2 209.766 210.148 1.00182
    fructose-bisphosphate aldolase a (ec 4.1.2.13) (muscle-type aldolase) (lung cancer antigen ny-lu-1). [swissprot;acc:p04075] 2907 ALDOA 0.00001 0.00001 1
    fructose-bisphosphate aldolase b (ec 4.1.2.13) (liver-type aldolase). [swissprot;acc:p05062] 2973 ALDOB
    fructose-bisphosphate aldolase c (ec 4.1.2.13) (brain-type aldolase). [swissprot;acc:p09972] 3087 ALDOC
    ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] 726 FTSJ3 244.495 232.419 1.05196
    fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954] 731 FH 208.874 219.708 1.05187
    fuse binding protein 3 (fragment). [sptrembl;acc:q92946] 2668 FUBP3 217.176 216.944 1.00107
    fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281] 1864 PUF60 203.071 200.89 1.01086
    fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476] 2124 AKTIP 221.248 222.788 1.00696
    fyve-finger-containing rab5 effector protein rabenosyn-5. [refseq;acc:nm_022340] 2998 ZFYVE20 0.00001 0.00001 1
    fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] 848 FZR1 147.211 153.371 1.04184
    g protein-coupled receptor 66. [refseq;acc:nm_006056] 2815 NMUR1 0.00001 0.00001 1
    g-rich sequence factor-1 (grsf-1). [swissprot;acc:q12849] 1855 GRSF1 217.891 215.542 1.0109
    g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] 1631 GSPT1 218.789 215.533 1.01511
    g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] 1582 CCNB1 168.098 170.844 1.01634
    g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] 1580 CCNB2 168.018 170.769 1.01637
    ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] 883 GABPA 227.596 219.017 1.03917

    Legend:
    - Rank is the rank after comparing the two networks
    - Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
    - Hugo is the HGNC identifier if it exists
    - Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
    - Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
    - Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
    - Filtered specifies whether we only included the high confidence microarry measurements or not.
    - http://analysis.yellowcouch.org/